Re: [Freesurfer] Common space

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 10/17/2023 11:55 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Good morning, I would be interested in observing regional differences in cortical thickness without using predefined regions. Howe

Re: [Freesurfer] Atrophy Maps on Coronal Slices

I'm not sure what you mean. Can you elaborate? On 10/17/2023 5:36 PM, Daniel Gutstein wrote: External Email - Use Caution Is there a methodology in FreeSurfer for creating atrophy maps and displaying them on individual coronal slices? Thank you. *Daniel Gutstein* Research Data Anal

Re: [Freesurfer] parallel processing of long-run fails

Hi Peter, I would suggest not to use ‘-parallel’. It is handled by recon-all to run multiple commands in parallel. It can run into collisions if they are not synchronized. These recon-all options ‘-threads <>’, ‘-openmp <>’, ‘-nthreads <>’ tell individual program to split the tasks and run the

Re: [Freesurfer] TR: Issues at the "tailarach_avi" transformation step of recon-all

The UNI scan will likely fail for the talairach. One thing you can try is -samseg-reg, which will compute the tal reg using samseg (which will be much more robust). However, it wont surprise me to see it fail somewhere else along the stream. On 10/18/2023 8:57 AM, Hensenne, Eva (Stud. FHML) wr

Re: [Freesurfer] .lta vs .dat questions

Hi Corinna, the two files should give the same vol2vol output. Can you send your command lines and pics of how they are different? The fscale was only used by the old tkregister program to control the brightness. doug On 10/18/2023 1:44 PM, Corinna Bauer wrote: External Email - Use

Re: [Freesurfer] mri_cvs_register failure

I'm not sure what happened. Have you checked the surface-based registration? Also check the talairach reg. On 10/19/2023 11:35 AM, Antonín Škoch wrote: External Email - Use Caution Dear experts, I have encountered an failure of mri_cvs_register --mov my_subject --mni The resulting

Re: [Freesurfer] fsxvfb error: Falling back to using screens root_visual

fsxvfb is just a script that sets up an env for running Xvfb. I wrote this script and got it working, but I'm not an expert on Xvfb, so you'll have to figure it out yourself. You can try to running another program that brings up an image (eg, fsxvfb glxgears) to make sure it is not a freeview t

Re: [Freesurfer] Loading surfaces

This usually means that you edited a recon, then reran recon-all but only partially leaving the surfaces out of sync. On 10/25/2023 11:40 AM, Huang, Yujing wrote: Hi Nicole, The error message indicated the number of vertices or the number of triangles don’t match in the two surface files it

Re: [Freesurfer] parallel processing of long-run fails

External Email - Use Caution Thank you for your reply! Best regards, Peter On Wed, Nov 8, 2023 at 2:41 PM Huang, Yujing wrote: > Hi Peter, > > > > I would suggest not to use ‘-parallel’. It is handled by recon-all to run > multiple commands in parallel. It can run into collisi

Re: [Freesurfer] extracting measurements from segment_subregions

Dear Victor, Thanks for letting us know. We’ll look into this ASAP. Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Victor (BIDMC - Keshavan - Psychiatry) Date: Wednesday, November 8, 2023 at 00:37 To: freesurfer@n

[Freesurfer] TRACULA Stat error: no pathway reconstructions found

External Email - Use Caution Hi FreeSurfers, I have successfully run trac-all -prep, -bedp, and -path on all of my files. However on two of my files when i ran trac-all -stat -c /Users/corpuscallosum/Desktop/TRACULA/RRD/R007A/R007A.txt and trac-all -stat -c on /Users/corpusca